Contacts of the helix formed by residues 190 - 212 (chain A) in PDB entry 2RCY
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 190 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A VAL* 4.4 0.9 - - - -
188A GLY 3.9 1.0 + - - -
189A LEU* 1.3 73.3 - - - +
191A ARG* 1.3 58.6 + - - +
192A GLU* 3.7 7.4 + - - +
193A LEU* 3.1 29.8 + - - +
194A SER* 2.9 31.3 + - - -
67D LYS* 5.8 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ILE* 4.1 16.2 - - + +
182A ASP* 2.7 29.9 + - - -
185A VAL* 3.8 42.8 - - + +
189A LEU 4.0 0.2 + - - -
190A SER* 1.3 73.2 - - - +
192A GLU* 1.3 63.6 + - - +
194A SER* 3.6 2.0 + - - -
195A LYS* 3.1 25.8 + - + +
217E GLN* 5.6 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A SER* 3.3 6.8 + - - +
191A ARG* 1.3 79.0 - - - +
193A LEU* 1.3 62.3 + - - +
195A LYS* 3.4 15.8 + - - +
196A ASN* 3.1 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LEU* 3.8 31.6 - - + -
190A SER* 3.1 19.6 + - - +
192A GLU* 1.3 75.6 - - - +
194A SER* 1.3 60.9 + - - +
196A ASN* 3.1 10.1 + - - +
197A LEU* 2.9 54.4 + - + +
152E HIS* 4.0 29.8 - - + +
154E ILE* 3.8 21.8 - - + -
158E ASP* 5.6 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ILE* 3.8 28.5 - - - -
184A GLY* 3.6 16.2 - - - -
185A VAL* 3.7 0.9 + - - -
189A LEU* 3.3 25.8 - - - +
190A SER 2.9 22.2 + - - -
191A ARG* 3.8 4.7 - - - -
193A LEU* 1.3 76.2 - - - +
195A LYS* 1.3 58.3 + - - +
197A LEU* 3.4 3.6 + - - +
198A VAL* 2.9 34.7 + - - +
165E ILE* 5.0 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ILE* 3.8 26.8 - - + +
191A ARG* 3.1 20.2 + - + +
192A GLU* 3.5 16.3 - - - +
193A LEU 3.2 0.2 - - - -
194A SER* 1.3 75.7 - - - +
196A ASN* 1.3 61.3 + - - +
198A VAL* 3.8 0.7 - - - +
199A LEU* 2.9 55.4 + - + +
209E VAL* 4.1 25.7 + - + -
210E LYS* 6.0 2.4 - - - +
216E VAL* 6.3 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A GLU* 3.1 33.4 + - - +
193A LEU* 3.5 10.6 - - - +
195A LYS* 1.3 82.5 - - - +
197A LEU* 1.3 58.4 + - - +
199A LEU* 4.0 6.1 - - - +
200A GLN* 3.1 33.3 + - - +
152E HIS* 4.2 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LEU* 4.2 15.0 - - + -
193A LEU* 2.9 29.6 + - + +
194A SER* 3.8 4.5 - - - +
196A ASN* 1.3 76.2 - - - +
198A VAL* 1.3 57.6 + - - +
200A GLN* 4.1 0.4 - - - -
201A THR* 2.5 35.0 + - - -
124E SER* 4.2 11.0 + - - +
125E PHE 5.0 0.2 - - - +
126E ILE* 3.9 25.1 - - + -
152E HIS* 3.6 30.1 - - + +
162E ALA* 4.0 22.4 - - + +
165E ILE* 4.4 10.1 - - + -
166E SER* 4.0 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ILE* 3.9 22.2 - - + +
180A LEU* 3.5 39.7 - - + +
181A ILE* 4.0 14.1 - - + +
194A SER* 2.9 23.0 + - - +
195A LYS* 3.8 3.1 - - - +
197A LEU* 1.3 75.0 - - - +
199A LEU* 1.3 60.9 + - - +
201A THR* 3.2 5.8 + - - -
202A ILE* 3.0 53.0 + - + +
165E ILE* 3.8 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ILE* 4.2 25.1 - - + -
195A LYS* 2.9 34.5 + - + +
196A ASN* 4.2 5.8 - - - +
198A VAL* 1.3 76.4 - - - +
200A GLN* 1.3 57.3 + - - +
202A ILE* 4.0 2.1 - - - -
203A LYS* 3.0 29.6 + - - +
206E VAL* 3.8 29.2 - - + +
209E VAL* 3.8 37.5 - - + -
210E LYS* 3.9 35.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ASN 3.1 18.9 + - - +
197A LEU* 4.4 2.0 - - - +
199A LEU* 1.3 74.8 - - - +
201A THR* 1.3 63.6 + - - +
203A LYS* 4.0 15.7 - - - +
204A GLY* 3.2 18.5 + - - -
115E ASN* 5.2 0.3 + - - -
122E GLU* 3.1 51.1 + - - +
123E GLY 3.4 19.2 + - - +
124E SER* 3.9 14.7 - - - +
149E GLY* 4.8 0.8 - - - -
150E ILE* 3.4 37.6 - - + +
210E LYS* 4.8 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LEU 2.5 24.5 + - - -
198A VAL* 3.2 6.7 + - - -
200A GLN* 1.3 77.6 - - - +
202A ILE* 1.3 53.7 + - - +
204A GLY* 4.1 0.7 - - - -
205A SER* 2.7 36.4 + - - +
115E ASN* 4.3 7.6 - - - +
117E PRO* 4.8 2.3 - - - +
124E SER* 4.0 2.4 - - - -
165E ILE* 3.8 4.7 + - - +
166E SER* 3.5 23.8 + - - +
169E GLY* 3.6 14.1 - - - +
170E PRO* 3.5 36.8 - - + -
173E VAL* 4.7 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A VAL* 5.4 1.6 - - + -
176A PHE* 4.3 15.5 - - + -
177A ILE* 3.6 33.0 - - + -
180A LEU* 4.4 2.7 - - + -
198A VAL* 3.0 32.9 + - + +
199A LEU* 4.0 4.3 - - - +
201A THR* 1.3 75.9 - - - +
203A LYS* 1.3 65.5 - - - +
205A SER* 3.2 2.3 + - - -
206A VAL* 3.0 24.6 + - + +
173E VAL* 3.8 31.9 - - + -
202E ILE* 3.4 32.1 - - + -
206E VAL* 3.7 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A LEU 3.0 19.0 + - - +
200A GLN* 3.9 13.0 - - - +
202A ILE* 1.3 75.4 - - - +
204A GLY* 1.3 62.6 + - - +
206A VAL* 3.7 2.4 + - - +
207A GLU* 3.3 36.5 + - - +
263A MG 3.5 16.1 - - - -
122E GLU* 3.5 32.2 + - + +
203E LYS* 5.7 6.9 - - - +
206E VAL* 4.9 4.9 - - + +
207E GLU* 5.0 9.5 + - - +
210E LYS* 3.9 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A GLN 3.2 10.8 + - - -
203A LYS* 1.3 76.9 - - - +
205A SER* 1.3 59.1 + - - +
207A GLU* 3.5 3.3 + - - +
208A MSE 3.1 32.2 + - - +
117E PRO* 3.5 12.9 - - - +
120E VAL* 4.3 0.5 - - - +
122E GLU* 3.5 33.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A THR 2.7 23.7 + - - -
202A ILE 3.2 4.7 + - - -
204A GLY* 1.3 74.1 - - - +
206A VAL* 1.3 63.8 + - - +
208A MSE 3.3 1.2 + - - -
209A VAL* 3.2 26.9 + - - +
117E PRO* 4.0 1.1 - - - +
170E PRO* 3.2 27.2 - - - +
173E VAL* 3.7 22.1 - - - +
174E TYR* 3.3 25.6 - - - -
177E ILE* 4.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ILE* 3.0 21.9 + - + +
203A LYS 4.0 2.2 - - - +
205A SER* 1.3 74.8 - - - +
207A GLU* 1.3 63.7 + - - +
209A VAL* 3.2 5.9 + - - +
210A LYS* 3.1 46.5 + - - +
263A MG 3.6 19.1 - - - -
177E ILE* 4.5 13.5 - - + -
199E LEU* 3.9 27.8 - - + +
202E ILE* 3.7 25.6 - - + -
203E LYS* 4.8 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A LYS* 3.3 32.4 + - - +
204A GLY* 3.7 6.7 - - - +
206A VAL* 1.3 79.8 - - - +
208A MSE 1.3 57.0 + - - +
210A LYS* 3.4 19.2 + - - +
211A LYS* 3.0 71.1 + - + +
120E VAL* 4.0 14.4 - - + +
122E GLU* 4.9 12.9 - - + +
203E LYS* 5.6 6.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A GLY 3.1 22.5 + - - +
205A SER 3.4 4.3 - - - +
206A VAL 3.3 0.4 - - - -
207A GLU* 1.3 76.1 - - - +
209A VAL* 1.3 56.5 + - - +
212A SER* 2.9 41.5 + - - -
219A LEU* 3.7 15.5 - - + -
265A GOL 3.4 41.7 - - - +
116E THR 3.8 6.7 - - - +
117E PRO* 3.7 21.8 - - + -
119E LEU* 3.8 15.5 - - + -
120E VAL* 3.7 30.3 - - + -
174E TYR* 3.2 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A SER 3.2 16.1 + - - +
206A VAL 3.2 6.7 + - - +
208A MSE 1.3 77.3 - - - +
210A LYS* 1.3 63.0 + - - +
212A SER* 3.7 11.6 - - - +
214A GLN 5.0 2.5 - - - +
216A VAL* 3.6 34.3 - - + +
219A LEU* 3.8 9.0 - - + -
174E TYR* 3.9 17.5 - - + -
177E ILE* 4.0 12.8 - - + -
195E LYS* 4.3 20.9 + - + -
199E LEU* 3.8 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ILE* 6.2 0.6 - - - +
206A VAL* 3.1 30.2 + - + +
207A GLU* 3.7 22.7 + - - +
208A MSE 3.3 0.2 - - - -
209A VAL* 1.3 78.6 - - - +
211A LYS* 1.3 63.4 + - + +
212A SER 4.3 2.4 - - - +
195E LYS* 6.3 1.1 - - - +
199E LEU* 3.8 30.0 + - + -
200E GLN* 4.7 5.6 + - - +
203E LYS* 3.5 35.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A GLU* 3.0 45.3 + - + +
210A LYS* 1.3 81.5 - - + +
212A SER* 1.3 63.4 + - - +
213A ASP 3.9 0.7 + - - -
120E VAL* 3.8 42.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A MSE 2.9 27.4 + - - +
209A VAL 3.7 11.3 - - - +
210A LYS 4.3 2.6 - - - +
211A LYS* 1.3 79.9 - - - +
213A ASP* 1.3 66.4 + - - +
214A GLN* 3.0 33.5 + - - +
219A LEU* 3.5 18.0 - - - +
265A GOL 5.3 0.6 + - - -
119E LEU* 6.2 1.3 - - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il